Chromosome 2 complete tiling path aCGH plots and mapping of the minimally deleted region. Genomic DNA was fragmented and labeled by random priming in a reaction containing a Cy3-dCTP (green test samples, APL) or a Cy5-dCTP (red reference samples, control DNA) fluorophore. Cohybridization with the test and reference DNA was performed overnight, followed by washing and imaging. The resultant green-to-red log₂ ratios were calculated and plotted by chromosomal location. Fifteen of the 35 samples analyzed with aCGH were previously analyzed with spectral karyotyping (SKY). We detected del(2) in 3 of 5 tumors that did not contain del(2) with SKY. Six of the 35 samples were previously analyzed with fluorescence in situ hybridization (FISH), and 1 PR+XRT sample that contained del(2) by FISH was not detected using aCGH. This sample contained del(2) in only 20% of cells, which is below the limit of detection using aCGH (M.J.W., R.E.R., T.J.L., unpublished observations, November 2006). (A) Log₂ plot from an APL sample with a normal chromosome 2. (B-D) APL samples with interstitial deletions on chromosome 2 produce a negative log₂ ratio for BAC probes located within the deletion. Arrows indicate deletion boundaries. (E) Twenty-five APL samples from various genotypes of mice contained del(2) by aCGH. Vertical bars indicate the boundaries of the interstitial deletions. Dashed lines indicate the boundaries of del(2) based on a radiation-induced AML model (84-105 megabases) that used simple sequence length polymorphisms to map deletion end points.⁶  Gray shaded rectangle (90-101 megabases) identifies the minimally deleted region (MDR) defined by aCGH. PU.1 is located within the aCGH defined MDR, whereas CD44 and WT1 genes are located distal to the telomeric border.